Skip to main content


Figure 1 | BMC Bioinformatics

Figure 1

From: Ultra-Structure database design methodology for managing systems biology data and analyses

Figure 1

Abstraction layers of the Ultra-Structure approach. The "deep structure" (bottom box) abstracts the fundamental concepts of the system. It is implemented as tables in a standard relational database system. It serves to constrain the structure of rules that can be added to the system, known collectively as the "middle structure" (middle box). These rules, stored as rows in database tables, in turn drive the execution of generalized software code called "animation procedures", which act to generate the "surface structure", or the real world manifestation of the system (top box). It is this easily-perceived but constantly changing level of surface structure that is generally modeled in traditional ER design. The end user (shown at top) interacts with this aspect of the system.

Back to article page